Transcriptomics

Dataset Information

2

A compendium of RNA-binding motifs for analysis of gene regulation


ABSTRACT: RNA binding proteins are key regulators of gene expression, yet only a small fraction of these proteins has been functionally characterized. Here, we report the first large-scale analysis of the RNA motifs recognised by RNA binding proteins, encompassing 205 distinct proteins from 24 diverse eukaryotes. The sequence specificities of RBPs display deep evolutionary conservation, such that the recognition preferences for a large fraction of metazoan RNA binding proteins can be inferred from the sequences of their binding domains. The motifs we identify in vitro correlate well with in vivo RNA-binding data. Moreover, we can associate them with distinct functional roles in diverse types of post-transcriptional regulation, enabling new insights into the functions of RNA binding proteins in both normal physiology and in human disease. These data provide an unprecedented global view of RBPs and their targets and constitute an invaluable resource for defining post-transcriptional regulatory mechanisms in eukaryotes. Here, we analyze the RNA-binding preferences of 205 distinct RNA-binding proteins from 24 different eukaryotes, using RNAcompete. In this assay, purified GST-tagged RBPs are incubated with an excess of RNA pool and bound RNA from individual pulldowns are directly labeled, hybridized to a custom Agilent 244K microarray, and analyzed computationally to identify RNA-binding motifs.

ORGANISM(S): synthetic construct  

SUBMITTER: Anita H Corbett   Mihai Albu  Xiao Li  Quaid D Morris  Seth M Kelly  Hilal Kazan  Brendan J Frey  Ally Yang  Christopher A Yarosh  Richard A Anderson  Elissa P Lei  Mei Qiao  Kristen W Lynch  Timothy R Hughes  Ryan K Dale  Manuel Irimia  Russ P Carsten  Behnam Nabet  Debashish Ray  Rakesh S Laishram  Fabio Piano  Hong Zheng  Weimin Li  Kate B Cook  Matthew T Weirauch  Andrew G Fraser  Sarah A Smith  Leah H Matzat  Benjamin J Blencowe  Luiz O Penalva  Hong Na  Serge Gueroussov  Hamed S Najafabadi  Howard D Lipshitz  Desirea Mecenas 

PROVIDER: E-GEOD-41235 | ArrayExpress | 2013-05-10

SECONDARY ACCESSION(S): GSE41235PRJNA176377

REPOSITORIES: GEO, ArrayExpress

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